The processing of genetic information in all cells often involves the ordered assembly of nucleoprotein complexes that subsequently catalyze reactions in a highly regulated and precise manner. Factors contributing to this process include sequence-specific DNA binding proteins that are unique for a particular reaction or type of reactions (e.g., RNA polymerase, specific control proteins), non-specific (or weakly sequence-specific) DNA binding proteins that facilitate or specifically regulate many unrelated reactions, and the higher-order structure of DNA (e.g., supercoiling, chromatin structure). A theme of our work is to attempt to integrate these factors into a comprehensive understanding of individual model reactions. We will continue with a detailed investigation of the Hin-catalyzed site-specific DNA inversion reaction from Salmonella. The goals are to determine the molecular structures of the reaction intermediates, the process by which Fis activates the Hin recombinase, and the mechanism of DNA exchange. The role of Fis in the Hin reaction will be contrasted with the primarily DNA architectural function of Fis combined with the phage-specific Xis protein in regulating phage lambda site-specific recombination. Cellular levels of Fis in E. coil vary under different growth conditions, from being the most abundant nucleoid-associated protein to being near absent. We will assess the role of Fis in controlling global gene expression patterns to gain a broad physiological understanding of regulation by Fis. Detailed studies on specific regulatory regions will also continue, particularly with respect to elucidating the nature of Fis-RNA polymerase interactions. The HMG1/2 DNA binding and bending proteins are one of the most abundant constituents of eukaryotic chromatin, although their specific biological activities are poorly understood. We will investigate how their DNA binding properties relate to their functional roles in different reactions with particular emphasis on S. cerevisiae NHP6A.